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71  structures 6272  species 0  interactions 13495  sequences 85  architectures

Family: Lysine_decarbox (PF03641)

Summary: Possible lysine decarboxylase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Possible lysine decarboxylase Provide feedback

The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR031100

The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG and pyrimidine/purine nucleotide 5'-monophosphate nucleosidase ygdH. LOG converts inactive cytokinin nucleotides to the biologically active free-base forms [ PUBMED:17287810 , PUBMED:19837870 ]. YgdH may catalyse the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base [ PUBMED:27941785 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan SLOG (CL0349), which has the following description:

Members of the SLOG superfamily were shown in bacteria and plants to cleave modified AMPs to release the base as cytokinins, which function as growth-stimulating hormones in plants. Known family members such as DprA is a member of the recombination-mediator protein family, dedicated to natural bacterial transformation [1]. This clan includes members such as the classical LOG family which generates cytokinin-like molecules, the Smf/DprA family which binds single-stranded (ss)DNA and interacts with RecA during transformation and recombination and the molybdenum cofactor-binding (MoCoBD) family. The SLOG domain adopts a three-layered alpha/beta sandwich Rossmannoid fold with a characteristic substrate-binding loop rich in glycine and small residues in the standard location between strand-1 and helix-1. It is suggested that the SLOG superfamily is likely to encompass dual functions, with certain versions serving as (oligo)nucleotide sensors and others as enzymes that operate on nucleotides [2].

The clan contains the following 13 members:

cpYpsA DNA_processg_A DUF3412 LD_cluster2 LD_cluster3 LDcluster4 LSDAT_euk LSDAT_prok Lysine_decarbox STALD TPALS YAcAr YpsA

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(26)
Full
(13495)
Representative proteomes UniProt
(51618)
RP15
(1425)
RP35
(6265)
RP55
(13027)
RP75
(21842)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(13495)
Representative proteomes UniProt
(51618)
RP15
(1425)
RP35
(6265)
RP55
(13027)
RP75
(21842)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(26)
Full
(13495)
Representative proteomes UniProt
(51618)
RP15
(1425)
RP35
(6265)
RP55
(13027)
RP75
(21842)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_741 (release 7.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 26
Number in full: 13495
Average length of the domain: 131.60 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 52.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 132
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lysine_decarbox domain has been found. There are 71 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0EYI1 View 3D Structure Click here
A0A0R0EZ50 View 3D Structure Click here
A0A0R0GBA6 View 3D Structure Click here
A0A0R0JIT3 View 3D Structure Click here
A0A0R0K2S3 View 3D Structure Click here
A0A0R4J2X8 View 3D Structure Click here
A0A0R4J4S8 View 3D Structure Click here
A0A1D6E5Y3 View 3D Structure Click here
A0A1D6K2U3 View 3D Structure Click here
A0A1D6NEC0 View 3D Structure Click here
A4HWA1 View 3D Structure Click here
A4HXF6 View 3D Structure Click here
A4IB94 View 3D Structure Click here
B4F8H8 View 3D Structure Click here
B4FH85 View 3D Structure Click here
B4FR76 View 3D Structure Click here
B6T9H8 View 3D Structure Click here
B6TTZ3 View 3D Structure Click here
B7E7M8 View 3D Structure Click here
B9F166 View 3D Structure Click here
C0P5X3 View 3D Structure Click here
C0PDT4 View 3D Structure Click here
C4JAR1 View 3D Structure Click here
C6T0I5 View 3D Structure Click here
C6T8B6 View 3D Structure Click here
C6TA03 View 3D Structure Click here
C6TIK3 View 3D Structure Click here
C6TLU1 View 3D Structure Click here
I1JGJ6 View 3D Structure Click here
I1K8D8 View 3D Structure Click here
I1KYF9 View 3D Structure Click here
I1L5N4 View 3D Structure Click here
I1L9I5 View 3D Structure Click here
I1L9R4 View 3D Structure Click here
I1LL44 View 3D Structure Click here
I1LTK5 View 3D Structure Click here
I1M4J3 View 3D Structure Click here
I1MX94 View 3D Structure Click here
K7M5X4 View 3D Structure Click here
K7TM25 View 3D Structure Click here
O05306 View 3D Structure Click here
P0ADR8 View 3D Structure Click here
P47044 View 3D Structure Click here
Q0DFG8 View 3D Structure Click here
Q0JBP5 View 3D Structure Click here
Q2G0B7 View 3D Structure Click here
Q4CYG8 View 3D Structure Click here
Q54UC5 View 3D Structure Click here
Q5AJ69 View 3D Structure Click here
Q5BPS0 View 3D Structure Click here
Q5TKP8 View 3D Structure Click here
Q5ZC82 View 3D Structure Click here
Q6F2U6 View 3D Structure Click here
Q7XDB8 View 3D Structure Click here
Q84M85 View 3D Structure Click here
Q84MC2 View 3D Structure Click here
Q851C7 View 3D Structure Click here
Q8GW29 View 3D Structure Click here
Q8H7U8 View 3D Structure Click here
Q8I1V0 View 3D Structure Click here
Q8L8B8 View 3D Structure Click here
Q8LBB7 View 3D Structure Click here
Q8LR50 View 3D Structure Click here
Q8RUN2 View 3D Structure Click here
Q9LFH3 View 3D Structure Click here
Q9LYV8 View 3D Structure Click here
Q9XH06 View 3D Structure Click here